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Open Access Open Badges Technical Note

RCDI/eRCDI: a web-server to estimate codon usage deoptimization

Pere Puigbò1*, Lluís Aragonès2 and Santiago Garcia-Vallvé3

Author Affiliations

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

2 Department of Microbiology, University of Barcelona, 08028 Barcelona, Spain

3 Department of Biochemistry and Biotechnology, Nutrigenomics Research Group, Rovira i Virgili University, 43007 Tarragona, Spain

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BMC Research Notes 2010, 3:87  doi:10.1186/1756-0500-3-87

Published: 31 March 2010



The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome.


RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at webcite.


This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression.